MCL coexpression mm9:671

Phase1 CAGE Peaks

	Short description
Mm9::chr14:122864041..122864099,-	p@chr14:122864041..122864099 -
Mm9::chr14:122864676..122864708,-	p1@Zic5
Mm9::chr14:122873661..122873686,+	p@chr14:122873661..122873686 +
Mm9::chr14:122873694..122873710,+	p@chr14:122873694..122873710 +
Mm9::chr14:122879279..122879285,+	p@chr14:122879279..122879285 +
Mm9::chr9:91259711..91259725,-	p@chr9:91259711..91259725 -
Mm9::chr9:91260248..91260259,-	p4@Zic1
Mm9::chr9:91262990..91263011,-	p@chr9:91262990..91263011 -
Mm9::chr9:91263173..91263220,+	p2@Zic4
Mm9::chr9:91273474..91273484,+	p11@Zic4
Mm9::chr9:91275527..91275544,+	p@chr9:91275527..91275544 +

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0007417	central nervous system development	0.000483665690904929
GO:0001843	neural tube closure	0.000498947244351965
GO:0014020	primary neural tube formation	0.000498947244351965
GO:0001841	neural tube formation	0.000498947244351965
GO:0001839	neural plate morphogenesis	0.000498947244351965
GO:0001838	embryonic epithelial tube formation	0.000498947244351965
GO:0001840	neural plate development	0.000498947244351965
GO:0021915	neural tube development	0.000568641857073429
GO:0016331	morphogenesis of embryonic epithelium	0.000636282393872113
GO:0003677	DNA binding	0.000636282393872113
GO:0007399	nervous system development	0.000835223444455235
GO:0002009	morphogenesis of an epithelium	0.00136167516678533
GO:0035239	tube morphogenesis	0.00181898416272182
GO:0003676	nucleic acid binding	0.00213504303258981
GO:0007420	brain development	0.00243345122482529
GO:0048598	embryonic morphogenesis	0.00256023272294392
GO:0035295	tube development	0.00256023272294392
GO:0016337	cell-cell adhesion	0.0025884509832289
GO:0043009	chordate embryonic development	0.00269954463698739
GO:0009792	embryonic development ending in birth or egg hatching	0.00269954463698739
GO:0005634	nucleus	0.00625387709903602
GO:0008589	regulation of smoothened signaling pathway	0.00703697243384536
GO:0048731	system development	0.00703697243384536
GO:0048869	cellular developmental process	0.00703697243384536
GO:0030154	cell differentiation	0.00703697243384536
GO:0009790	embryonic development	0.00815239420749265
GO:0008270	zinc ion binding	0.0084646283988294
GO:0048856	anatomical structure development	0.00910520032603384
GO:0007275	multicellular organismal development	0.0116707777989934
GO:0022610	biological adhesion	0.0116707777989934
GO:0007155	cell adhesion	0.0116707777989934
GO:0007224	smoothened signaling pathway	0.0116707777989934
GO:0048066	pigmentation during development	0.0117203371206961
GO:0046914	transition metal ion binding	0.0125989430938281
GO:0032502	developmental process	0.0221024338513604
GO:0043231	intracellular membrane-bound organelle	0.0221024338513604
GO:0043227	membrane-bound organelle	0.0221024338513604
GO:0043169	cation binding	0.0288932550287507
GO:0009653	anatomical structure morphogenesis	0.0318776641924248
GO:0030900	forebrain development	0.0319765146532927
GO:0043229	intracellular organelle	0.0319765146532927
GO:0043226	organelle	0.0319765146532927
GO:0046872	metal ion binding	0.0322470960645324
GO:0043167	ion binding	0.0334005799442731
GO:0048513	organ development	0.0386898252973023
GO:0032501	multicellular organismal process	0.045169113728162

Relative expression of the co-expression cluster over median <br>Analyst:

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Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
CNS neuron (sensu Vertebrata)	6.87e-13	23
neuroblast (sensu Vertebrata)	6.87e-13	23
neural cell	5.12e-11	43
ectodermal cell	1.38e-10	44
neurectodermal cell	1.38e-10	44
non-terminally differentiated cell	1.02e-08	49
neuron	4.62e-08	33
neuronal stem cell	4.62e-08	33
neuroblast	4.62e-08	33
electrically signaling cell	4.62e-08	33

Uber Anatomy

Ontology term	p-value	n
neurectoderm	9.21e-20	64
neural plate	9.21e-20	64
presumptive neural plate	9.21e-20	64
central nervous system	1.74e-19	73
nervous system	1.39e-18	75
regional part of nervous system	1.70e-18	54
neural tube	6.46e-18	52
neural rod	6.46e-18	52
future spinal cord	6.46e-18	52
neural keel	6.46e-18	52
ectoderm-derived structure	8.68e-18	95
ectoderm	8.68e-18	95
presumptive ectoderm	8.68e-18	95
ecto-epithelium	1.56e-16	73
regional part of brain	5.02e-13	46
pre-chordal neural plate	1.09e-12	49
brain	1.48e-12	47
future brain	1.48e-12	47
posterior neural tube	1.09e-10	12
chordal neural plate	1.09e-10	12
structure with developmental contribution from neural crest	1.82e-10	92
anterior neural tube	1.27e-09	40
regional part of forebrain	3.11e-09	39
forebrain	3.11e-09	39
future forebrain	3.11e-09	39
gray matter	2.05e-08	34
spinal cord	4.56e-07	6
dorsal region element	4.56e-07	6
dorsum	4.56e-07	6
regional part of spinal cord	9.34e-07	5
gray matter of spinal cord	9.34e-07	5

TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
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